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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaaggctttaaacttttaatctagttactgtatgacccagatggcgttaaacggagactgaatttttcttcacccctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG

Basic information

species Zea mays
transcript GRMZM2G080722_T01
intron # 6
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71772931|gb|DR970854.1|DR970854
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCATTATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACNAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149072625|gb|EE160853.2|EE160853
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|5819352|gb|AI987558.1|AI987558
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAACCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|84980246|gb|DW530595.1|DW530595
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACAATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|76019176|gb|DT946346.1|DT946346
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|31348993|gb|CD433350.1|CD433350
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAGCTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|18649501|gb|BM498320.1|BM498320
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|6827118|gb|AW330761.1|AW330761
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|89252698|gb|DY624484.1|DY624484
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|108954172|gb|EC365037.1|EC365037
EST:     TCTTAGCAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149076048|gb|EE164622.2|EE164622
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|211208256|gb|FL334762.1|FL334762
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|71772930|gb|DR970853.1|DR970853
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|32934185|gb|CF038997.1|CF038997
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149072626|gb|EE160854.2|EE160854
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|76019175|gb|DT946345.1|DT946345
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|31364491|gb|CD448846.1|CD448846
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAGCTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|32931043|gb|CF035855.1|CF035855
EST:     ATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: ATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|211509923|gb|FL437420.1|FL437420
EST:     GATCTGATATCATACTCACCATGCACCAR                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: GATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|18450417|gb|BM428695.1|BM428695
EST:     TAAGGTAGAGTTCGTTGGTGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCCGATATTGCACAAAAAGCCGAACA
genomic: -AAGG-AGAGTTCGTTGG-GGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGG-CGATATTGCACAAAAAGCCGAACA
EST: gi|71771232|gb|DR969169.1|DR969169
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149051827|gb|EE155954.2|EE155954
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAAGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAG
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAG
EST: gi|211395747|gb|FK956104.1|FK956104
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGC
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGC
EST: gi|149051826|gb|EE155953.2|EE155953
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149076047|gb|EE164621.2|EE164621
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCCCCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 135

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgacccagatggcgttaaacggagactgaatttttcttcacccctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG
                                tttttcttcacccctt  CT-rich tract
                              aatttttctt  TA-rich tract